Package Bio :: Package Blast :: Module Applications :: Class NcbideltablastCommandline
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Class NcbideltablastCommandline

source code

                     object --+                
                              |                
Application.AbstractCommandline --+            
                                  |            
          _NcbibaseblastCommandline --+        
                                      |        
                  _NcbiblastCommandline --+    
                                          |    
                  _Ncbiblast2SeqCommandline --+
                                              |
                                             NcbideltablastCommandline

Create a commandline for the NCBI BLAST+ program deltablast (for proteins).

This is a wrapper for the deltablast command line command included in the NCBI BLAST+ software (not present in the original BLAST).

>>> from Bio.Blast.Applications import NcbideltablastCommandline
>>> cline = NcbideltablastCommandline(query="rosemary.pro", db="nr",
...                               evalue=0.001, remote=True)
>>> cline
NcbideltablastCommandline(cmd='deltablast', query='rosemary.pro', db='nr', evalue=0.001, remote=True)
>>> print(cline)
deltablast -query rosemary.pro -db nr -evalue 0.001 -remote

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

Instance Methods [hide private]
 
__init__(self, cmd='deltablast', **kwargs)
Create a new instance of a command line wrapper object.
source code

Inherited from _Ncbiblast2SeqCommandline (private): _validate

Inherited from Application.AbstractCommandline: __call__, __repr__, __setattr__, __str__, set_parameter

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='deltablast', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)